Structural Genomics @CNAG · CRG


We have contributed to the following books:



Publications

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Bibliography last updated on: 2018-12-05


There are 104 publications of article type

104.-Miguel-Escalada, I.,  Bonàs-Guarch, S.,  Cebola, I.,  Ponsa-Cobas, J.,  Mendieta-Esteban, J. ,  Rolando, D.,  Javierre, B.M.,  Atla, G.,  Farabella, I.,  Morgan, C.C.,  García-Hurtado, J.,  Beucher, A.,  Morán, I.,  Pasquali, L.,  Ramos, M.,  Appel, E.V.R.,  Linneberg, L.,  Gjesing, A.P.,  Witte, D.R.,  Pedersen, O.,  Grarup, N.,  Ravassard, P.,  Mercader, J.M.,  Torrents, D.,  Piemonti, L.,   Berney, T.,  de Koning E.,  Kerr-Conte, J.,  Pattou, F.,  Hansen, T.,   Marti-Renom, M.A.,  Fraser, P. and Ferrer, J.
"Human pancreatic islet 3D chromatin architecture provides insights into the genetics of type 2 diabetes"
BioRxiv (2018) preprint   
BioRxiv
  
103.-Goodstadt, M. and Marti-Renom, M.A.
"Biovisualization of the Genome, from Data Analysis and Hypothesis Generation to Communication and Learning"
Journal of Molecular Biology (2018) in press   
Journal NCBI Related
  
102.-Nir, G.,  Farabella, I.,  Pérez Estrada, C.,   Ebeling, C.G.,  Beliveau, B.J.,  Sasaki, H.M.,  Lee, S.H.,  Nguyen, S.C.,  McCole, R.B.,  Chattoraj, S.,  Erceg, J.,  Abed, J.A.,  Martins, N.M.C.,   Nguyen, H.Q.,  Hannan, M.A.,  Russell, S.,  Durand, N.C.,  Rao, S.S.P.,  Kishi, J.Y.,  Soler-Vila, P.,  Di Pierro, M.,  Onuchic, J.N.,  Callahan, S.,  Schreiner, J.,  Stuckey, J.,  Yin, P.,  Lieberman Aiden, E.,  Marti-Renom, M.A. and Wu, C.T.
"Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling"
PLOS Genetics (2018) in press   
BioRxiv
  
101.-Pascual-Reguant. L.,  Blanco, E.,  Galan, S.,  Le Dily, F.,  Cuartero, Y.,  Serra-Bardenys, G.,  di Carlo, V.,  Iturbide, A.,  Cebrià-Costa, J.P.,  Nonell, L.,  García de Herreros, A.,  Di Croce, L.,  Marti-Renom, M.A. and Peiró, S.
"Genome-wide mapping of lamin B1 reveals the existence of dynamic and functional euchromatin lamin B1 domains (eLADs) during epithelial-to-mesenchymal transition (EMT)."
Nature Communications (2018) 9(1) 3420  
Journal NCBI Related
  
100.-Mas, G.,  Blanco, E.,  Ballaré, C.,  Sansó, M.,  Spill, Y.G.,  Hu, D.,  Aoi, Y.,  Le Dily, F.,  Shilatifard, A.,  Marti-Renom, M.A. and Di Croce, L.
"Promoter bivalency favors an open architecture of the stem cell genome"
Nature Genetics (2018) 50 1452–1462  
Journal NCBI Related
  
99.-Stadhouders, R.,  Vidal, E.,  Serra, F.,  Di Stefano, B.,  Le Dily, F.,  Quilez, J.,  Gomez, A.,  Collombet, S.,  Berenguer, C.,  Cuartero, Y.,  Hecht, J.,  Filion, G.,  Beato, M.,  Marti-Renom, M.A. and Graf, T.
"Transcription factors orchestrate dynamic interplay between genome topology and gene regulation during cell reprogramming."
Nature Genetics (2018) 50 238–249  
Journal NCBI Related BioRxiv
  
98.-Kojic, A.,  Cuadrado, A.,  Koninck, A.M.,  Gomez-Lopez, G.,  Rodriguez-Corsino, M.,  Le Dily, F.,  Marti-Renom, M.A. and Losada, A.
"Distinct roles of cohesin-SA1 and cohesin-SA2 in 3D chromosome organization"
Nature Structural and Molecular Biology (2018) 25 496–504  
Journal NCBI Related BioRxiv
  
97.-Beekman R.,  Chapaprieta V.,  Russiñol, N.,  Vilarrasa-Blasi, R.,   Verdaguer-Dot, N.,  Martens, J.H.A.,  Duran-Ferrer, M.,  Kulis, M.,  Serra, F.,  Javierre,. B.M.,  Wingett, S.W.,  Clot, G.,  Queirós, A.C.,  Castellano, G,  Blanc, J.,  Gut, M.,  Merkel, A.,  Heath, S.,  Vlasova, A.,  Ullrich, S.,  Palumbo, E.,  Enjuanes, A.,   Martín-García, D.,  Beà, S.,  Pinyol, M.,  Aymerich, M.,  Royo, R.,  Puiggros, M.,  Torrents, D.,  Datta, A.,  Lowy, E.,  Kostadima, M.,  Roller, M.,  Clarke, L.,  Flicek, P.,  Agirre, X.,  Prosper, F.,  Baumann, T.,  Delgado, J.,  López-Guillermo, A.,  Fraser, P.,  Yaspo, M-L.,  Guigó, R.,  Siebert, R.,  Marti-Renom, M.A.,  Puente, X.S.,  López-Otín, C.,  Gut, I.,  Stunnenberg, H.G.,  Campo, E. and Martin-Subero, J.I.
"The reference epigenome and regulatory chromatin landscape of chronic lymphocytic leukemia"
Nature Medicine (2018) 24 868–880  
Journal NCBI Related
  
96.-Vidal, E.,  Le Dily, F.,  Quilez, J.,  Stadhouders, R.,  Cuartero, Y.,  Graf, T.,  Marti-Renom, M.A.,  Beato, M. and Filion, G.
"OneD: increasing reproducibility of Hi-C Samples with abnormal karyotypes"
Nucleic Acids Research (2018) 04 e49  
Journal NCBI Related BioRxiv
  
95.-Marti-Renom, M.A.,  Almouzni, G.,  Bickmore, W.A.,  Bystricky, K.,  Cavalli, G.,  Fraser, P.,  Gasser, S.M.,  Heard, E.,  Nicodemi, M.,  Orozco, M.,  Pombo, A. and Torres-Padilla, M-E.
"4D Nucleome: challenges and guidelines towards data and model standards"
Nature Genetics (2018) 50 1352–1358  
Journal NCBI Related
  
94.-Spill, Y.G.,  Castillo, D. and Marti-Renom, M.A.
"Binless normalization of Hi-C data provides significant interaction and difference detection independently of resolution."
BioRxiv (2017) preprint   
BioRxiv
  
93.-Di Giovanni, F.,  Di Stefano, M.,  Baù, D.,  Carey, L.B.,  Marti-Renom, M.A. and Mendoza, M.
"The spatial position of budding yeast chromosomes affects gene expression"
BioRxiv (2017) preprint   
BioRxiv
  
92.-Morf, J.,  Wingett, S.W.,  Farabella, I.,  Cairns, J.,   Furlan-Magaril, M.,  Liu, X.,  Craig, F.F.,  Andrews, S.,  Marti-Renom, M.A. and Fraser, P.
"Spatial RNA proximities reveal a bipartite nuclear transcriptome and territories of differential density and transcription elongation rates."
BioRxiv (2017) preprint   
BioRxiv
  
91.-Trussart, M.,  Yus, E.,  Martinez, S.,  Baù, D.,  Tahara, Y.O.,  Pengo, T.,  Kretschmer, S.,  Swoger, J.,  Miyata, M.,  Marti-Renom, M.A.,  Lluch-Senar, M. and Serrano, L.
"Defined chromosome structure in a genome-reduced bacterium, Mycoplasma pneumoniae."
Nature Communications (2017) 8 14665  
Journal NCBI Related
  
90.-Martínez-Jiménez, F.,  Overington, J.P.,  Al-Lazikani, B. and Marti-Renom, M.A.
"Rational design of non-resistant targeted cancer therapies."
Scientific Reports (2017) 7 46632  
Journal NCBI Related
  
89.-Quilez, J.,  Vidal, E.,  Le Dily, F.,  Serra, F.,  Cuartero, Y.,  Stadhouders, R.,  Graf, T.,  Marti-Renom, M.A.,  Beato, M. and Filion, G.
"Parallel sequencing lives, or what makes large sequencing projects successful"
GigaSciences (2017) 6 1-6  
Journal NCBI Related BioRxiv
  
88.-Goodstadt, M. and Marti-Renom, M.A.
"Challenges for visualizing three-dimensional data in genomic browsers"
FEBS Letters (2017) 591 2505–2519   
Journal NCBI Related
  
87.-Serra, F.,  Baù, D.,  Goodstadt, M.,  Castillo, D.,  Filion, F. and Marti-Renom, M.A.
"Automatic analysis and 3D-modelling of Hi-C data using TADbit reveals structural features of the fly chromatin colors"
PLOS Computational Biology (2017) 13(7) e1005665  
Journal NCBI Related BioRxiv
  
86.-Cattoni, D.I.,  Cardozo-Gizz, A.M.,  Georgieva, M.,  Di Stefano, M.,  Valeri, A.,  Chamousset, D.,  Houbron, C.,  Dejardin, S.,  Fiche, J-B.,  Marti-Renom, M.A.,  Bantignies, F.,  Cavalli, G. and Nollmann, M.
"Single-cell absolute contact probability detection reveals that chromosomes are organized by modulated stochasticity"
Nature Communications (2017) 8 1753  
Journal NCBI Related BioRxiv
  
85.-Le Dily, F.,  Serra, F. and Marti-Renom, M.A.
"3D modeling of chromatin structure: is there a way to integrate and reconcile single cell and population experimental data?"
WIREs Comput Mol Sci (2017) e1308  
Journal
  
84.-Baeza-Delgado, C.,  Von Heijne, G.,  Marti-Renom, M.A. and Mingarro, I.
"Biological insertion of computationally designed short transmembrane segments."
Scientific Reports (2016) 6 23397   
Journal NCBI Related
  
83.-Bogu, G.K.,   Vizan, P.,  Stanton, L.W.,  Beato, M.,  Di Croce, L. and Marti-Renom, M.A.
"Chromatin and RNA maps reveal regulatory long noncoding RNAs in mouse."
Mol Cell Biol (2016) 36 (5) 809-819  
Journal NCBI Related
  
82.-Martínez-Jiménez, F. and Marti-Renom, M.A.
"Should network biology be used for drug discovery?"
Expert Opinion on Drug Discovery (2016) 10.1080/17460441.201  
Journal NCBI Related
  
81.-Serra, F.,  Di Stefano, M.,  Spill, Y.G.,  Cuartero, Y.,  Goodstadt, M.,  Baù, D. and Marti-Renom, M.A.
"Restraint-based three-dimensional modeling of genomes and genomic domains"
FEBS Letters (2015) 589 (20) 2987–2995  
Journal NCBI Related
  
80.-Junier, I.,  Spill, Y.G.,   Marti-Renom, M.A.,  Beato, M. and le Dily, F.
"On the demultiplexing of chromosome capture conformation data"
FEBS Letters (2015) 589 (20) 3005–3013  
Journal NCBI Related
  
79.-Trussart, M.,  Serra, F.,  Baù, D.,  Junier, I.,  Serrano, L. and Marti-Renom, M.A.
"Assessing the limits of restraint-based 3D modeling of genomes and genomic domains."
Nucleic Acids Research (2015) 43 (7) 3465-3477  
Home Journal NCBI Related
  
78.-Sali, A.,  Berman, H.,  Schwede, T.,  Trewhella, J.,  Kleywegt, G.,  Burley, S.,  Markley, J.,  Nakamura, H.,  Adams, P.,  Bonvin, A.,  Chiu, W.,  Dal Peraro, M.,  Di Maio, F.,  Ferrin, T.,  Grünewald, K.,  Gutmanas, A.,  Henderson, R.,  Hummer, G.,  Iwasaki, K.,  Johnson, G.,  Lawson, C.,  Meiler, J.,  Marti-Renom, M.A.,  Montelione, G.,  Nilges, M.,  Nussinov, R.,  Patwardhan, A.,  Rappsilber, J.,  Read, R.,  Saibil, H.,  Schröder, G.,  Schwieters, C.,  Svergun, C.,  Topf, D.,  Ulrich, M.,  Velankar, E. and Westbrook, S.
"Outcome of the First wwPDB Hybrid / Integrative Methods Task Force Workshop"
Structure (2015) 23(7) 1156–1167  
Journal NCBI Related
  
77.-Belton, J-M.,  Lajoie, B.R.,  Audibert, S.,  Cantaloube, S.,  Lassadi, I.,  Goiffon, I.,  Baù, D.,  Marti-Renom, M.A.,  Bystricky, K. and Dekker, J.
"The conformation of yeast chromosome III is mating type-dependent and controlled by the recombination enhancer."
Cell Reports (2015) 13 1–13  
Journal NCBI Related
  
76.-Martínez-Jiménez, F. and Marti-Renom, M.A.
"Ligand-target prediction by structural network biology using nAnnoLyze."
PLOS Computational Biology (2015) 11(3) e1004157  
Home Journal NCBI Related
  
75.-Rebollo-Lopez, MJ.,  Lelievre, J.,  Alvarez-Gomez, D.,  Castro-Pichel, J.,  Martínez-Jiménez, F.,  Papadatos, G.,  Kumar, V.,  Colmenarejo, G.,  Mugumbate, G.,  Hurle, M.,  Barroso, V.,  Young, R.J.,  Martinez-Hoyos, M.,  Bates, R.H.,  Lopez-Roman, E.M.,  Mendoza-Losana, A.,  Brown, J.R.,  Alvarez-Ruiz, E.,  Marti-Renom, M.A.,  Overington, J.P.,  Cammack, N.,  Ballell, LL. and Barros-Aguire, D.
"Release of 50 new, drug-like compounds and their computational target predictions for open source anti-tubercular drug discovery"
PLOS ONE (2015) 10(12) e0142293  
Journal NCBI Related
  
74.-Dufour, D. and Marti-Renom, M.A.
"Software for predicting the 3D structure of RNA molecules."
WIREs Comput Mol Sci (2014) 5 (1) 56–61  
Journal
  
73.-Le Dily, F.,  Baù, D.,  Pohl, A.,  Vicent, G.P.,  Serra, F.,  Soronellas, D.,  Castellano, G.,  Wright, R.H.G,  Ballare, C.,  Filion, G.,  Marti-Renom, M.A. and Beato, M.
"Distinct structural transitions of chromatin topological domains correlate with coordinated hormone-induced gene regulation"
Genes & Dev. (2014) 28 2151-2162  
Journal NCBI Related BioRxiv
  
72.-Martínez-Jiménez, F.,  Papadatos, G.,  Yang, L.,  Wallace, I.M.,  Kumar, V.,  Pieper, U.,  Sali, A.,  Brown, J.R.,  Overington, J.P. and Marti-Renom, M.A.
"Target prediction for an open access set of compounds active against Mycobacterium tuberculosis"
PLOS Computational Biology (2013) 9(10) e1003253  
Journal NCBI Related
  
71.-Baeza-Delgado, C.,  Marti-Renom, M.A. and Mingarro, I.
"Structure-based statistical analysis of transmembrane segments"
European Biophysics Journal (2013) 42 199-207  
Journal NCBI Related
  
70.-Köser, C.U.,  Bryant, J.M.,  Becq, J.,  Török, M.E.,  Ellington, M.J.,  Marti-Renom, M.A.,  Carmichael, A.J.,  Parkhill, J.,  Smith, G.P. and Peacock, S.J.
"Whole-genome sequencing for rapid susceptibility testing of M. tuberculosis"
NEJM (2013) 369 290-292  
Journal NCBI Related
This article has been highlighted in Nature here and here.
  
69.-Kemena, C.,  Bussotti, G.,  Capriotti, E.,  Marti-Renom, M.A. and Notredame, C
"Using tertiary structure for the computation of highly accurate multiple RNA alignments with the SARA-Coffee package"
Bioinformatics (2013) 29 1112-1119  
Journal NCBI Related
  
68.-López-Pelegrín, M.,  Cerdà-Costa, N.,  Martínez-Jiménez, F.,  Cintas, A.,  Canals, A.,  Peinado, J.R.,  Marti-Renom, M.A.,  López-Otín, C.,   Arolas, J.L. and Gomis-Rüth, F.X.
"A novel family of soluble minimal scaffolds provides structural insight into the catalytic domains of integral-membrane metallopeptidases."
JBC (2013) 288 21279–21294  
Journal NCBI Related
  
67.-Dekker, J.,  Marti-Renom, M.A. and Mirny, L.A.
"Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data"
Nature Reviews Genetics (2013) 14 390–403  
Journal NCBI Related
  
66.-Bañó-Polo, M.,  Baeza-Delgado, C.,  Orzáez, M.,  Marti-Renom, M.A.,  Abad, C. and Mingarro, I.
"Polar/Ionizable residues in transmembrane segments: effects on helix-helix packing."
PLoS ONE (2012) 7 e44263  
Journal NCBI Related
  
65.-Baù, D. and Marti-Renom, M.A.
"Genome structure determination via 3C-based data integration by the Integrative Modeling Platform"
Methods (2012) 58 300–306  
Journal NCBI Related
  
64.-Marti-Renom, M.A. and Mirny L.
"Bridging the resolution gap in structural modeling of 3D genome organization"
PLoS Computational Biology (2011) 7 e1002125  
Journal NCBI Related
  
63.-Feuerriegel, I.,  Köser, C.,  Baù, D.,  Rüsch-Gerdes, S.,  Summers, D.,  Archer, J.,  Marti-Renom, M.A. and Niemann, S.
"Impact of fgd1 and ddn diversity in Mycobacterium tuberculosis complex on in vitro susceptibility to PA-824"
Antimicrobial Agents and Chemotherapy (2011) 55 5718-5722  
Journal NCBI Related
  
62.-Umbarger, M.A.,  Toro, E.,  Wright, M.A.,  Porreca, G.J.,  Baù, D.,  Hong, S-H.,  Fero, M.J.,  Zhu, J.,  Marti-Renom, M.A.,  McAdams, J.H.,  Shapiro, L.,  Dekker, J. and Church, G.M.
"The three-dimensional architecture of a bacterial genome and Its alteration by genetic perturbation"
Molecular Cell (2011) 44 252–264  
Journal NCBI Related Fac1000
This article has been highlighted in a Journal Club at the NRMCB and in a News & Views at NRM.
  
61.-Martínez-Gil, L. ,  Saurí, A.,  Marti-Renom, M.A. and Mingarro, I
"Membrane protein integration into the ER"
FEBS Journal (2011) 278 3846–3858  
Journal NCBI Related
  
60.-Capriotti, E.,  Norambuena, T,  Marti-Renom, M.A. and Melo, F.
"All-atom knowledge-based potential for RNA structure prediction and assessment"
Bioinformatics (2011) 27 1086-1093  
Journal NCBI Related
  
59.-Sanyal, A.,  Baù, D.,  Marti-Renom, M.A. and Dekker, J.
"Chromatin globules: a common motif of higher-order chromosome structure?"
Current Opinion in Cell Biology (2011) 23 325–33  
Journal NCBI Related
  
58.-Bañó-Polo, M. ,  Baldin, F.,  Tamborero, S.,  Marti-Renom, M.A. and Mingarro, I
"N-Glycosylation efficiency is determined by the distance to the C-terminus and the amino acid preceding an Asn-Ser-Thr sequon."
Protein Science (2011) 20 179–186  
Journal NCBI Related
  
57.-Baù, D. and Marti-Renom, M.A.
"Structure determination of genomic domains by satisfaction of spatial restraints"
Chromosome Research (2011) 19 (1) 25  
Journal NCBI Related
  
56.-Baù, D.,  Sanyal, A.,  Lajoie, B.R.,  Capriotti, E.,   Byron, M.,   Lawrence J.B.,  Dekker, J. and Marti-Renom, M.A.
"The three-dimensional folding of the α-globin gene domain reveals formation of chromatin globules"
Nature Structural and Molecular Biology (2011) 18 107-114  
Journal NCBI Related
This article has been highlighted in a Technology Feature at the Nature Journal.
  
55.-Capriotti, E. and Marti-Renom, M.A.
"Quantifying the relationship between sequence and three-dimensional structure conservation in RNA"
BMC Bioinformatics (2010) 11 322  
Journal NCBI Related
  
54.-Madhusudhan, MS.,  Webb, B.,  Marti-Renom, M.A.,  Eswar, N. and  Sali, A.
"Alignment of multiple protein structures based on sequence and structure features."
PEDS (2009) 22 569-574   
Home Journal NCBI Related
  
53.-Capriotti, E. and Marti-Renom, M.A.
"SARA: a server for function annotation of RNA structures"
Nucleic Acids Research (2009) 37 W260-5  
Home Journal NCBI Related
  
52.-Fornes, O.,  Aragues, R.,  Espadaler, J.,  Marti-Renom, M.A.,  Sali, A. and Oliva, B.
"ModLink+: Improving fold recognition by using protein-protein interactions"
Bioinformatics (2009) 25 1506-12  
Home Journal NCBI Related
  
51.-Orti, L.,   Carbajo, R.J.,   Pieper, U.,  Eswar, N.,  Maurer, S.M.,  Rai, A.K.,  Taylor, G.,  Todd, M.H.,  Pineda-Lucena, A.,  Sali, A. and Marti-Renom, M.A.
"A kernel for open source drug discovery in tropical diseases"
PLoS Neglected Tropical Diseases (2009) 3 e18  
Home Journal NCBI Related
  
50.-Orti, L.,   Carbajo, R.J.,   Pieper, U.,  Eswar, N.,  Maurer, S.M.,  Rai, A.K.,  Taylor, G.,  Todd, M.H.,  Pineda-Lucena, A.,  Sali, A. and Marti-Renom, M.A.
"A kernel for the Tropical Disease Initiative"
Nature Biotechnology (2009) 27 320-321  
Home Journal NCBI Related This is a Correspondence to the Editor.
  
49.-Pieper, U.,  Eswar, N.,  Webb, B.M.,  Eramian, D.,  Kelly, L.,  Barkan, D.T.,  Carter, H.,  Mankoo, P.,  Karchin, R.,  Marti-Renom, M.A.,  Davis, F.P. and Sali, A.
"MODBASE, a database of annotated comparative protein structure models, and associated resources."
Nucleic Acids Research (2009) 37 D347-D354  
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48.-Espadaler, J.,  Eswar, N.,  Querol, E.,  Aviles, F.X.,  Sali, A.,  Marti-Renom, M.A. and Oliva, B.
"Prediction of enzyme function by combining sequence similarity and protein interactions"
BMC Bioinformatics (2008) 9(1) 249  
Journal NCBI Related
  
47.-Panjkovich, A.,  Melo, F. and Marti-Renom, M.A.
"Evolutionary potentials: structure specific knowledge-based potentials exploiting the evolutionary record of sequence homologs"
Genome Biology (2008) 9 R68  
Journal NCBI Related
  
46.-Capriotti, E. and Marti-Renom, M.A.
"Computational RNA structure prediction "
Current Bioinformatics (2008) 3 (1) 32-45  
Home Journal
  
45.-Capriotti, E.,  Arbiza, L.,  Casadio, R.,  Dopazo, J.,  Dopazo, H. and Marti-Renom, M.A.
"The use of estimated evolutionary strength at the codon level improves the prediction of disease related protein mutations in human."
Human Mutation (2008) 29 (1) 198-204  
Home Journal NCBI Related
  
44.-Capriotti, E. and Marti-Renom, M.A.
"RNA structure alignment by a unit-vector approach"
Bioinformatics (2008) 24 i112-i118  
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43.-Eswar, N.,  Webb, B.,  Marti-Renom, M.A. ,  Madhusudhan, M.S.,  Eramian, D.,  Shen, M-Y.,  Pieper, U. and Sali A.
"Comparative Protein Structure Modeling Using MODELLER. "
Current Protocols in Protein Science (2007) 2.9 (Nov 2007) 2.9.1-2.9.31  
Journal NCBI Related pdf This is an updated and revised version of the CPPS unit published in Nov. 2002
  
42.-Marti-Renom, M.A.,   Rossi, A.,  Al-Shahrour, F.,   Davis, F.,  Pieper, U.,  Dopazo, J. and Sali, A.
"The AnnoLite and AnnoLyze programs for comparative annotation of protein structures"
BMC Bioinformatics (2007) 8 (Suppl 4) S4  
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41.-Stanley, W.A.,  Fodor, K.,   Marti-Renom, M.A.,  Schliebs, W. and Wilmanns, M.
"Protein translocation into peroxisomes by ring-shaped import receptors"
FEBS Letters (2007) 581 4795-802  
Journal NCBI Related
  
40.-Marti-Renom, M.A.,  Pieper, U.,  Madhusudhan, M.S.,  Rossi, A.,  Eswar, N.,  Davis, F.P.,  Al-Shahrour, F.,  Dopazo, J. and  Sali A.
"DBAli tools: mining the protein structure space"
Nucleic Acids Research (2007) 35 W393-W397  
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39.-Aragues, R.,   Sali, A.,  Bonet, J.,  Marti-Renom, M.A. and Oliva, B.
"Characterization of protein hubs by inferring interacting motifs from protein interactions"
PLoS Computational Biology (2007) 3(9) e178  
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38.-Melo, F. and Marti-Renom, M.A.
"Accuracy of sequence alignment and fold assessment using reduced amino acid alphabets"
Proteins (2006) 63 986-995  
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37.-Kepler, T.,  Marti-Renom, M.A.,  Maurer, S.M.,  Rai A.K.,  Taylor, G. and Todd, M.H
"Open Source Research - The power of Us"
Aust. J. Chem. (2006) 59 291-294  
Journal
  
36.-Eswar, N.,  Webb, B.,  Marti-Renom, M.A. ,  Madhusudhan, M.S.,  Eramian, D.,  Shen, M-Y.,  Pieper, U. and Sali A.
"Comparative Protein Structure Modeling with MODELLER"
Current Protocols in Bioinformatics (2006) 5.6 (Dec 2006) 5.6.1-5.6.30  
Journal NCBI Related pdf This is an updated and revised version of the CPBI unit published in Nov 2003
  
35.-Topf, M.,  Baker, ML.,  Marti-Renom, MA.,  Chiu, W and Sali, A
"Structure characterization of assembly components by iterative comparative modeling and cryoEM density fitting"
J. Mol. Biol. (2006) 357(5) 1655-68  
Home Journal NCBI Related
  
34.-Pieper, U.,  Eswar, N.,   Davis, F.,   Braberg, H.,  Madhusudhan, M.S.,,  Rossi, A.,  Marti-Renom, M.A.,  Karchin, R.,  Webb, B.,  Eramian, D.,  Shen, M-Y.,  Kelly, L.,  Melo, F. and Sali, A.
"MODBASE, a database of annotated comparative protein structure models, and associated resources"
Nucleic Acids Research (2006) 34 D291-295  
Home Journal NCBI Related
  
33.-Madhusudhan, MS.,  Marti-Renom, MA.,  Sanchez, R. and Sali, A.
"Variable gap penalty for protein sequence-structure alignment"
PEDS (2006) 19 129-133  
Home Journal NCBI Related
  
32.-Rossi, A.,  Marti-Renom, M.A. and Sali, A.
"Localization of binding sites in protein structures by optimization of a composite scoring function"
Protein Science (2006) 15 2366-2380  
Home Journal NCBI Related
  
31.-Eramian, D.,  Shen, M-Y.,  Devos, D.,  Melo, F.,  Sali, A. and Marti-Renom, M.A.
"A composite score for predicting errors in protein structure models"
Protein Science (2006) 15 1653-1666  
Journal NCBI Related
  
30.-McMahon, S.A.,  Miller, J.L.,  Lawton, J.A.,  Kerkow, D.E.,  Hodes, A.,  Marti-Renom, M.A.,  Doulatov, S.,  Eswar, N.,  Sali, A.,  Miller, J.F. and Ghosh, P.
"The C-type lectin fold as a scaffold for massive sequence variation"
Nature Structural and Molecular Biology (2005) 12 886-892  
Journal NCBI Related Fac1000 recommended
  
29.-Espadaler, J.,  Aragues, R.,  Eswar, N.,  Marti-Renom, M.A.,  Querol, E.,  Aviles, F.X.,  Sali, A. and Oliva, B.
"Detecting remote homology by sequence similarity and protein-protein interactions."
Proc. Natl. Acad. Sci. USA. (2005) 102 7151-7156  
Journal NCBI Related
  
28.-Mirkovic, N.,  Marti-Renom, M.A.,  Weber, B.L.,  Sali, A. and Monteiro, A.N.A.
"Structure-based assessment of missence mutations in human BRCA1: Implications for breast and ovarian cancer predisposition."
Cancer Research (2004) 64 3790-3797  
Home Journal NCBI Related
  
27.-Pieper, U.,  Eswar, N.,  Braberg, H.,  Madhusudhan, MS.,  Davis, FP.,  Stuart, AC.,  Mirkovic, N.,  Rossi, A.,  Marti-Renom, MA.,  Fiser, A.,  Webb, B.,  Greenblatt, D.,  Huang, CC.,  Ferrin, TE. and Sali, A.
"MODBASE, a database of annotated comparative protein structure models, and associated resources."
Nucleic Acids Res (2004) 32 D217-22  
Home Journal NCBI Related
  
26.-Marti-Renom, M.A.,  Madhusudhan, M.S. and Sali, A.
"Alignment of protein sequences by their profiles"
Protein Science (2004) 13 1071-1087  
Journal NCBI Related
  
25.-Marti-Renom, M.A.,   Fiser, A.,  Madhusudhan, M.S.,  John, B.,  Stuart, A.,  Eswar, N.,  Pieper, P.,  Shen, MY. and Sali, A.
"Modeling protein structure from its sequence"
Current Protocols in Bioinformatics. Ed: John Wiley & Sons, Inc. (2003) 5.1 (Nov 2003) 5.1.1-5.1.22  
Journal pdf This is an updated and revised version of the original CPBI unit published in Jan 2003
  
24.-Marti-Renom, M.A.
"Protein Structure Modeling for Structural Genomics"
Business Briefing: Future Drug Discovery (2003) June 59-63  
Journal pdf
  
23.-Marti-Renom, M.A.,  Yercovich, B. and Sali, A.
"Modeling protein structure from its sequence."
Current Protocols in Bioinformatics. Ed: John Wiley & Sons, Inc. (2003) 5.1 (Jan 2003) 5.1.1-5.1.22  
Journal pdf
  
22.-Koh, I-Y. Y. ,  Eyrich, V.A.,  Marti-Renom, M.A.,  Przybylski, D.,  Madhusudhan, M.S.,  Narayanan, E.,  Graña, O.,  Pazos, F.,  Valencia, A.,  Sali, A. and Rost, B.
"EVA: evaluation of protein structure prediction servers"
Nucleic Acids Research (2003) 31 3311-3315  
Home Journal NCBI Related
  
21.-Narayanan, E.,  John, B.,  Mirkovic, N.,  Fiser, A.,  Ilyin, V.,  Pieper, U.,  Stuart, A.C.,  Marti-Renom, M.A.,  Madhusudhan, M.S.,  Yerkovich, B. and Sali A.
"Tools for comparative protein structure modeling and analysis"
Nucleic Acids Research (2003) 31 3375-3380.  
Home Journal NCBI Related
  
20.-Ilyin, VA.,  Pieper, U.,  Stuart, AC.,  Marti-Renom, MA.,  McMahan, L. and Sali, A.
"ModView, visualization of multiple protein sequences and structures."
Bioinformatics (2003) 19 165-6  
home journal MedLine related pdf
  
19.-Iverson, GM.,  Reddel, S.,  Victoria, EJ.,  Cockerill, KA.,  Wang, YX.,  Marti-Renom, MA.,  Sali, A.,  Marquis, DM.,  Krilis, SA. and Linnik, MD.
"Use of Single Point Mutations in Domain I of beta(2)-Glycoprotein I to Determine Fine Antigenic Specificity of Antiphospholipid Autoantibodies."
J Immunol (2002) 169 7097-7103  
Journal NCBI Related pdf
  
18.-Martí-Renom, M.A.,  Madhusudhan, M.S.,  Fiser, A.,  Rost, B. and Sali, A.
"Reliability of assessment of protein structure prediction methods"
Structure (2002) 10 435--440  
journal NCBI Related pdf Fac1000 recommended
  
17.-Sali, A.,  Martí-Renom, M.A.,  Madhusudhan, M.S.,  Fiser, A. and Rost, B.
"Reply To Moult et al."
Structure (2002) 10 292--293  
Journal pdf
  
16.-Martí-Renom, M.A.,  Yercovich, B. and Sali, A.
"Comparative Protein Structure Prediction"
Current Protocols in Protein Science (2002) 1 2.9.1-2.9.22,  
Journal pdf
  
15.-Eyrich, V.,  Martí-Renom, M.A.,  Przybylski, D.,  Fiser, A.,  Madhusudhan, M.S.,  Pazos, F.,  Valencia, A.,  Sali, A. and Rost, B.
"EVA: continuous automatic evaluation of protein structure prediction servers."
Bioinformatics (2001) 17 1242-1243  
Home Journal NCBI Related
  
14.-Marti-Renom, MA.,  Ilyin, VA. and Sali, A.
"DBAli: a database of protein structure alignments."
Bioinformatics (2001) 17 746-7  
Home Journal NCBI Related
  
13.-Mas, JM.,  Aloy, P.,   Martí-Renom, M.A.,  Oliva, B.,  de Llorens, R.,  Aviles, FX. and Querol, E.
"Classification of protein disulphide-bridge topologies."
J Comput Aided Mol Des (2001) 15 477-87  
Journal NCBI Related
  
12.-Sánchez, R.,  Pieper, U.,  Melo, F.,  Eswar, N.,  Martí-Renom, M.A.,  Madhusudhan, M.S.,  Mirkovic, N. and Sali, A.
"Protein structure modeling for structural genomics"
Nat Struct Biol (2000) 7 Suppl 986--90  
Journal NCBI Related pdf
  
11.-Martí-Renom, M.A.,  Stote, R.H.,  Querol, E.,  Avilés, F.X. and Karplus, M.
"Structures of scrambled disulfide forms of the potato carboxypeptidase inhibitor predicted by molecular dynamics simulations with constraints."
Proteins (2000) 40 482--493  
Journal NCBI Related pdf
  
10.-Martí-Renom, M.A.,  Stuart, A.,  Fiser, A.,  Sánchez, R.,  Melo, F. and Sali, A.
"Comparative protein structure modeling of genes and genomes."
Annu Rev Biophys Biomol Struct (2000) 29 291--325  
Journal NCBI Related pdf
  
9.-Serra-Hartmann, X.,  Rebordosa, X.,  Piñol, J.,  Querol, E. and Martí-Renom, M.A.
"ASAP analysis of peptide composition."
Bioinformatics (2000) 16 1153--1154  
Home Journal NCBI Related pdf
  
8.-Aloy, P.,  Mas, J.M.,  Martí-Renom, M.A.,  Querol, E.,  Avilés, F.X. and Oliva, B.
"Refinement of modelled structures by knowledge-based energy profiles and secondary structure prediction: application to the human procarboxypeptidase A2."
J Comput Aided Mol Des (2000) 14 83--92  
Journal NCBI Related pdf
  
7.-Liedtke, W.,  Choe, Y.,  Martí-Renom, M.A.,  Bell, A.M.,  Denis, C.S.,  Sali, A.,  Hudspeth, A.J.,  Friedman, J.M. and Heller, S.
"Vanilloid receptor-related osmotically activated channel (VR-OAC), a candidate vertebrate osmoreceptor"
Cell (2000) 103 525--35  
Journal NCBI Related pdf
  
6.-Martí-Renom, M.A.
"ASAP, web server for analysis of peptide composition"
CCP11 Newsletters (1999) 9 2-3  
Home Journal PDF
  
5.-Martí-Renom, M.A.,  Stote, R.H.,  Querol, E.,  Avilés, F.X. and Karplus, M.
"Refolding of potato carboxypeptidase inhibitor by molecular dynamics simulations with disulfide bond constraints"
J Mol Biol (1998) 284 145--72  
Journal NCBI Related pdf
  
4.-Mas, J.M.,  Aloy, P.,  Martí-Renom, M.A.,  Oliva, B.,  Blanco-Aparicio, C.,  Molina, M.A.,  de, Llorens, R.,  Querol, E. and Avilés, F.X.
"Protein similarities beyond disulphide bridge topology"
J Mol Biol (1998) 284 541--8  
Journal NCBI Related pdf
  
3.-Stote ,R.H.,  Martí-Renom, M.A.,  Querol, E.,  Aviles, F.X. and Karplus, M.
"Molecular dynamics simulations of the unfolding and refolding of potato carboxypeptidase inhibitor"
ABSTR PAP AM CHEM S (1998) 216 U272  
Journal
  
2.-Martí-Renom, M.A.,  Mas, J.M.,  Aloy, P.,  Querol, E.,  Avilés, F.X. and Oliva, B.
"Statistical Analysis of the Loop-geometry on a Non-redundant Database of Proteins"
J Mol Model (1998) 11 347--354  
journal pdf
  
1.-Martí-Renom, M.A.,  Mas, J.M.,  Oliva, B.,  Querol, E. and Avilés, F.X.
"Effects of counter-ions and volume on the simulated dynamics of solvated proteins. Application to the activation domain of procarboxypeptidase B"
Protein Eng (1998) 11 881--90  
Journal NCBI Related pdf
  

There are 7 publications of book type

7.-Dufour, D. and Marti-Renom, M.A.
"Modeling of RNA sequences"
(2013) Springer Edition 2013 p1566-1569  
Journal Amazon
  
6.-Dufour, D.,  Capriotti, E. and Marti-Renom, M.A.
"Computational methods for RNA structure prediction and analysis."
(2013) PanStanford Publishing 1st edition   
Amazon
  
5.-Marti-Renom, M.A.,  Capriotti, E.,  Shindyalov, I. and Bourne, P.
"Structural Comparison and Alignment. In: Structural Bioinformatics. "
(2009) Wiley-Blackwell, New Jersey. USA. 2nd Edition   
Amazon
  
4.-Engelen, S. and Marti-Renom, M.A.
"Open source drug discovery: The Tropical Disease Initiative. In: In Sickness and in Health. The Future of Medicine: Added Value and Global Access."
(2009) VUBPRESS, Brussels, Belgium   
Journal
  
3.-Capriotti, E. and Marti-Renom, M.A.
"Assessment of protein structure predictions. In: Computational Structural Biology. "
(2008) World Scientific Publishing Company. New Jersey. USA.   
Amazon
  
2.-Madhusudhan, M.S.,  Marti-Renom, M.A.,   Eswar, N.,  John, B,  Pieper, U.,   Karchin, R.,  Shen, M-Y and Sali, A
"Comparative protein structure prediction. In: The Proteomics Protocols Handbook."
(2005) Humana Press Inc. Totowa, NJ. 835-864  
Journal Amazon
  
1.-Barbadilla, A.,  Naveira, H.,  Santos, M.,  Martí-Renom, M.A. and Peris, F.
"Introducción al BMDP en VAX/VMS"
(1992) UAB, Bellaterra, Spain   
Practices book for Biostatistics at 3rd grade in Biology studies
  

There are 6 publications of phdthesis type

6.-Baeza-Delgado, C.,  Marti-Renom, M.A. and Mingarro, I.
"On the design of optimally inserted transmembrane helices"
(2017) Valencia, Spain   
  
5.-Bogu, G.K.,  Marti-Renom, M.A. and Guigó, R.
"Understanding the transcriptional landscape of non-coding genome (lncRNAs and repetitive elements) in mammals"
(2017) Barcelona, Spain   
  
4.-di Giovanni, F.,  Marti-Renom, M.A. and Mendoza, M.
"The impact of chromosome positioning in nuclear functions"
(2016) Barcelona, Spain   
  
3.-Martínez-Jiménez, F. and Marti-Renom, M.A.
"Structural study of the therapeutic potential of protein-ligand interactions"
(2016) Barcelona, Spain   
  
2.-Trussart, M.,  Marti-Renom, M.A. and Serrano, L.
"Structure determination of Mycoplasma pneumoniae genome"
(2015) Barcelona, Spain   
  
1.-Martí-Renom, M.A.
"On the Unfolding and Refolding of Potato Carboxypeptidase Inhibitor"
(1999) Bellaterra, Spain   
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